1. Field of the Invention
The present invention relates to the fields of chemistry and chemical and molecular biology, and to processes in which there is a direct or indirect qualitative or quantitative measurement or test of a material which contains at least one protein species. More particularly, the invention relates to subject matter in which a measurement or test utilizes at least one protein species in a specific binding protein or other specific ligand-receptor binding test or assay.
2. Description of Related Art
DNA-binding proteins (such as basic-region zippers, arc repressors, and type II restriction endonucleases) often harness dimer self-assembly (formation of protein-protein homo- or hetero-dimers) to recognize and bind with high affinity to their cognate duplex targets via bidentate interactions (K. S. Thompson, C. R. Vinson, E. Freire. Biochemistry. 1993, 32, 5491-5496; J. U. Bowie, R. T. Sauer. Biochemistry. 1989, 28, 7139-7143; and A. Pingoud, A. Jeltsch. Nucleic Acids Res. 2001, 29, 3705-3727, each of which is incorporated by reference herein in its entirety). In an elegant role reversal, the research groups of Hamilton and Neri, have independently developed synthetically modified DNA duplexes (which are not aptamers) that can bind to target proteins in a 2:1 fashion. For duplex DNA derived bidentate protein-binders see: S. Melkko, J. Scheuermann, C. E. Dumelin, D. Neri. Nat. Biotechnol. 2004, 22, 568-574; K. I. Sprint, D. M. Tagore, A. D. Hamilton, Bioorg. Med. Chem. Lett. 2005, 15, 3908-3911; S. Melkko, Y. Zhang, C. E. Dumelin, J. Scheuermann, D. Neri, Angew. Chem. Int. Ed. 2007, 46, 4671-4674; and J. Scheuermann, C. E. Dumelin, S. Melkko, Y. Zhang, L. Mannocci, M. Jaggi, J. Sobek, D. Neri, Bioconjugate Chem. 2008, 19, 778-785, each of which is incorporated by reference herein in its entirety. In particular, these researchers demonstrated that DNA duplex self-assembly results in the projection of synthetic protein-binding fragments in a bidentate manner (FIG. 3A), leading to the selective sequestration (via interaction with the synthetic protein-binding fragments) of a variety of proteins including carbonic anhydrase (Melkko, et al., Nat. Biotechnol. 2004), streptavidin (Sprint, et al., Bioorg. Med. Chem. Lett. 2005), trypsin (Melkko, et al., Angew. Chem. Int. Ed. 2007), and matrix metalloproteinase (Scheuermann, et al., Bioconjugate Chem. 2008). In addition, higher order intermolecular quadruplex based tetradentate protein-binders (FIG. 3B) have been recently introduced: D. M. Tagore, K. I. Sprint, S. Fletcher, J. Jayawickramarajah, A. D. Hamilton. Angew. Chem. Int. Ed. 2007, 46, 223-225, incorporated by reference herein in its entirety. In each of these systems, the chelate effect plays a central role in enhancing the affinity and selectivity of the multidentate binders above and beyond their individual monomeric components (which project only one synthetic protein-binding unit). See, e.g., S. Melkko, C. E. Dumelin, J. Scheuermann, D. Neri. Chem. Biol. 2006, 13, 225-231, incorporated by reference herein in its entirety. As used in this application, “chelate” and “chelation” refers to the caliper- or claw-like action of at least two functional groups which recognize and “grab” a target in at least two places. However, in each of the prior art systems described in FIGS. 3A and 3B, it is the synthetic protein-binding fragments that interact with protein targets, not the DNA fragments attached to the synthetic protein-binding fragments. Self-assembled oligonucleotides (ODNs) that form, say, a duplex or an intermolecular tetraplex as shown in FIGS. 3A and 3B, are not considered to be aptamers.
Aptamers are, generally, single stranded nucleic acids (DNA or RNA) that can fold into unique structures and bind to specific target molecules. As a result of their remarkable specificity and affinity, aptamers are currently pursued as tools for diagnostic applications. See: Hesselberth, J.; Robertson, M. P.; Jhaveri, S. D.; Ellington, A. D. “In vitro selection of nucleic acids for diagnostic applications” Rev. Mol. Biotechnol. 2000, 74, 15-25, incorporated by reference herein in its entirety. These same attributes also make aptamers viable pharmaceutical agents when they are selected against proteins implicated in human disease. See, e.g., Proske, D.; Blank, M.; Buhmann, R.; Resch, A. “Aptamers-basic research, drug development, and clinical applications” Appl. Microbiol. Biotechnol. 2005, 69, 367-374, incorporated by reference herein in its entirety. For instance, aptamers have been developed against various growth factors including the platelet derived growth factor (PDGF) and the vascular endothelial growth factor (VegF). Bell, C.; Lynam, E.; Landfair, D. J.; Janjic, N.; Wiles, M. N. “Oligonucleotide NX1838 inhibits VegF165-mediated cellular responses in vitro” In Vitro Cell. Dev. Biol. Anim. 1999, 35, 533-542; Floege, J.; Ostendorf, T.; Janssen, U.; Burg, M.; Radeke, H. H.; Vargeese, C.; Gill, S. C.; Green, L. S.; Janjic, N. “Novel approach to specific growth factor inhibition in vivo: antagonism of platelet-derived growth factor in glomerulonephritis by aptamers” Am. J. Pathol. 1999, 154, 169-179, each of which is incorporated by reference herein in its entirety. In fact, an anti-VegF aptamer (Macugen®) has been approved by the FDA for treatment of age-related macular degeneration and is currently commercialized.
In addition to the development of traditional aptamer systems that bind to molecules of interest, recent work has focused on aptamer conjugates that utilize aptamer-based binding characteristics to control the function of complex systems. Famulok, M.; Hartig, J. S.; Mayer, G. “Functional aptamers and aptazymes in biotechnology, diagnostics, and therapy” Chem. Rev. 2007, 107, 3715-3743, incorporated by reference herein in its entirety. An example of such an aptamer conjugate is shown in FIG. 1, which shows an allosteric aptamer linked to a ribozyme module (termed “aptazyme”) to regulate ribozyme activity. See, e.g., Najafi-Shoushtari, S.; Famulok, M. “Competitive regulation of modular allosteric aptazymes by a small molecule and oligonucleotide effector” RNA 2005, 11, 1514-1520, incorporated by reference herein in its entirety. Aptamers can be combined with ribozymes to self-cleave in the presence of their target molecule. As shown in FIG. 1, two halves (labeled “A” and “B”) of a hairpin ribozyme are tethered to a central flavin mononucleotide (FMN) binding aptamer (denoted by the wavy line between “A” and “B”). In the absence of FMN, the aptamer region remains unstructured (as represented by the wavy line), producing spatial separation of ribozyme domains A and B. Because the interaction of these two domains is critical for ribozyme activity (e.g., cleavage of the FMN-binding aptamer), the system remains in the “Inactive Form” in the absence of FMN. In marked contrast, addition of FMN leads to a conformational change in the aptamer moiety, via interaction between FMN and the FMN-aptamer, that brings domains A and B of the hairpin-ribozyme complex in close proximity. The conformational switch of the aptamer domain to a stem-loop structure upon binding to FMN, as shown in the “Active Form” on the right-hand side of FIG. 1, produces an activated aptazyme and leads to cleavage of the bound RNA at a specific site (denoted by the dashed arrow) with concomitant production of cleaved RNA substrate.
Another important aptamer system that has gained attention is the thrombin binding aptamer (Wu, Q.; Tsiang, M.; Sadler, J. E. “Localization of the single-stranded DNA binding site in the thrombin anion-binding exosite” J. Biol. Chem. 1992, 267, 24408-24412, incorporated by reference herein in its entirety), which undergoes a transition from a random coil to an intramolecular quadruplex upon binding to thrombin. Baldrich, E.; O'Sullivan, C. K. “Ability of thrombin to act as a molecular chaperone, inducing formation of quadruplex structure of thrombin-binding aptamer” Anal. Biochem. 2005, 341, 194-197, incorporated by reference herein in its entirety. Nucleic acids that are rich in guanine (e.g., the thrombin binding aptamer) are capable of forming four-stranded structures called quadruplexes (also known as G-quadruplexes, G-tetrads, or G4-DNA). Quadruplexes contain guanine nucleotides arranged in a square (a tetrad, with the guanines denoting the corners of the square), and may be stabilized by monovalent cations (especially potassium ion, K+) in the center of two tetrads or by binding to specific proteins (e.g., thrombin). Quadruplexes can be formed by DNA, RNA, LNA (“locked nucleic acid”), and PNA (“peptide nucleic acid”), and may be intramolecular (i.e., a solitary strand), bimolecular (i.e., two separate strands), or tetramolecular (i.e., four separate strands). Depending upon the strand orientation, or the orientation of the parts that form the quadruplex, quadruplexes may be described as parallel or antiparallel.
The complex comprising thrombin binding aptamer bound to thrombin protein is characterized by a dissociation constant (Kd) in the micromolar range, and inhibits thrombin activity (see, e.g., Pagano; B. Martino, L.; Randazzo, A.; Giancola, C. Biophysical Journal, 2008, 562-569, incorporated by reference herein in its entirety). Thrombin (also known as activated Factor II) is a serine protease that not only initiates blood coagulation (by catalyzing fibrin formation) but also acts as a general pro-inflammatory agent by interacting with protease-activated receptors (PARs) present on cell-surfaces. Cocks, T. M.; Moffatt, J. D. “Protease-activated receptors: sentries for inflammation?” Trends. Pharmacol. Sci. 2000, 21, 103-108, incorporated by reference herein in its entirety. In particular, thrombin activates PAR-1. Trypsin is another serine protease that can activate PARs (PAR-2, in particular) and, not surprisingly, is also associated with inflammatory conditions. In addition to being upregulated under inflammatory conditions, these two proteinases (i.e., thrombin and trypsin) have recently been implicated in tumor metastasis and invasion. Given the similarity in function of these two proteases and their critical activity in many salient diseases, much effort has been devoted to the development of broad-spectrum small-molecule chemical compounds that inhibit the activities of both thrombin and trypsin simultaneously. These efforts, though, have met with limited success. See, e.g., Bhattacharya, A.; Smith, G. F.; Cohen, M. L. “Effect of LY287045, a thrombin/trypsin inhibitor, on thrombin and trypsin-induced aortic contraction and relaxation” J. Pharmacol. Exp. Ther. 2001, 297, 573-581, incorporated by reference herein in its entirety. However, development of small-molecules that can selectively inhibit only thrombin and trypsin and not inhibit other members of the serine-protease family has been a significant challenge. Furthermore, prolonged inhibition of these two proteases can lead to serious side-effects including severe bleeding and death.
While the example described in FIG. 1 clearly illustrates the power of allosteric aptamers when tethered to catalytically active ODNs (oligonucleotides), there has been no prior exploration of the potential for developing allosteric aptamers tethered to synthetic, protein-binding, small molecules. Such a chimeric molecule (wherein aptamers are judiciously functionalized with synthetic, protein-binding, small-molecules with appropriate spacers) would provide for a modular and versatile system whose protein-binding activity is responsive to external stimuli. Further these newly conceived chimeric systems are expected to be a significant boon for novel technologies in diagnostics and therapeutics.
The technical problem underlying the present invention was therefore to overcome these prior art difficulties by: a) providing methods of preparing a novel class of molecules—termed herein “apta-chelamers”—that are well-controlled binders of selected target proteins; and b) preparing functional embodiments of said molecules. The solution to this technical problem is provided by the embodiments characterized in the claims.